4C9F | pdb_00004c9f

Structure of SIGN-R1 in complex with Sulfodextran


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.233 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history

Literature

Structural Basis for Selective Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor Sign-R1

Silva-Martin, N.Bartual, S.G.Rodriguez, A.Ramirez, E.Chacon, P.Anthony, R.M.Park, C.G.Hermoso, J.A.

(2014) Structure 22: 1595

  • DOI: https://doi.org/10.1016/j.str.2014.09.001
  • Primary Citation Related Structures: 
    3ZHG, 4C9F, 4CAJ, 4CDH

  • PubMed Abstract: 

    SIGN-R1 is a principal receptor for microbial polysaccharides uptake and is responsible for C3 fixation via an unusual complement activation pathway on splenic marginal zone macrophages. In these macrophages, SIGN-R1 is also involved in anti-inflammatory activity of intravenous immunoglobulin by direct interaction with sialylated Fcs. The high-resolution crystal structures of SIGN-R1 carbohydrate recognition domain and its complexes with dextran sulfate or sialic acid, and of the sialylated Fc antibody provide insights into SIGN-R1’s selective recognition of a-2,6-sialylated glycoproteins. Unexpectedly, an additional binding site has been found in the SIGNR1 carbohydrate recognition domain, structurally separate from the calcium-dependent carbohydrate-binding site. This secondary binding site could bind repetitive molecular patterns, as observed in microbial polysaccharides, in a calcium-independent manner. These two binding sites may allow SIGNR1 to simultaneously bind both immune glycoproteins and microbial polysaccharide components, accommodating SIGN-R1’s ability to relate the recognition of microbes to the activation of the classical complement pathway.

Macromolecule Content 

  • Total Structure Weight: 65.59 kDa 
  • Atom Count: 4,680 
  • Modeled Residue Count: 531 
  • Deposited Residue Count: 536 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CD209 ANTIGEN-LIKE PROTEIN B
A, B, C, D
134Mus musculusMutation(s): 0 
UniProt
Find proteins for Q8CJ91 (Mus musculus)
Explore Q8CJ91 
Go to UniProtKB:  Q8CJ91
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8CJ91
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-6)-4-O-sulfo-alpha-D-glucopyranose
E, F
2N/A
Glycosylation Resources
GlyTouCan: G16612YC
GlyCosmos: G16612YC
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-4-O-sulfo-alpha-D-glucopyranose
G
4N/A
Glycosylation Resources
GlyTouCan: G91665XU
GlyCosmos: G91665XU

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GQ1

Query on GQ1



Download:Ideal Coordinates CCD File
V [auth D],
W [auth D],
X [auth D]
4-O-sulfo-alpha-D-glucopyranose
C6 H12 O9 S
LOTQRUGOUKUSEY-UKFBFLRUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A]
K [auth B]
L [auth B]
M [auth B]
N [auth B]
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
S [auth C],
U [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
P [auth C],
T [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.233 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.025α = 90
b = 97.959β = 120.86
c = 73.846γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary